Re: Yamaha 250?
I'll assume that besides the flat tires there is nothing else that is wrong on the bike at this point. This is the drill I do with new project bikes, it takes a few hours, but it is not something you need to be a master teck to do. when I started working on bikes i was only 16, and didn't have a clue about anything on a bike.
First step is exactly as you said, doing normal stuff like clean up the bike- air filter, oil and gas filters if they apply, drain and replace the oil (let the new oil soak into the clutch if it's a wet clutch for a few hours if nobody has turned it over in years, be sure to rotate them once in a while to soak them properly - the theory is that it can save your clutch - the oil probally settled on the bottom of the crankcase leaving part of the clutch disks out on the oil, drying them out over time).
New plug, new battery if needed (if it's used), drain any gas and use new, be sure to clean out the carb good - you may need to take it off the bike and take it apart to do it right. new coolant if it applies, lube the chassis and inspect it for anything it may need, see it the tires hold air, check for dryrot on them and any other rubber part, check the switches to make sure thay work, you may need to clean connectors and/or terminals in the electric system. Check brakes and clutch opperation, suspension, ect.....
Now, i think I got most of the drill down, this is when I try to start it, hopefully it runs good, but now is the time to see what else it needs, and how far you want to get into them - ride them as they are or to do a restoration.
If if the bike needs major repair it may not be worth it, but who knows, there are stories of people that pull their bike out from under a tarp after sitting for years and having them start the first kick, without going through all the stuff above.
good luck, and let us know how it turnes out.
83 ATC 250r (with many extra parts 4 sale), 83 ATC 185s, 89 zuki' 250sport.